Figure 3. Structural Principles of Ligand Recognition by Riboswitches.

(A–C) Schematic representations of a “straight” junctional fold (A), observed in type Ia riboswitches; an “inverse” junctional fold (B) from type Ib riboswitches; and a pseudoknot fold (C), which is characteristic for type II riboswitches. Pink and blue shading depict ligand binding sites and long-distance tertiary interactions, respectively. The magenta segment in helix P1 designates regions capable of alternative base pairing. Representative structures in ribbon representation for TPP (Serganov et al., 2006; Thore et al., 2006), THF (Huang et al., 2011; Trausch et al., 2011), and fluoride (Ren et al., 2012) riboswitches are shown under the corresponding fold schematics. Ligands are in red surface representation. Mg²⁺ cations are depicted by green spheres. 3WJ, three-way junction; PK, pseudoknot.

(D) Recognition of TPP by the TPP riboswitch. PP, pyrophosphate; Thi, thiazole; and APy, aminopyrimidine moieties. Mg²⁺ cations are shown with coordination bonds depicted by green sticks. Water molecules are shown as red spheres.